6L49

H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA

Exp. Method	EM
Resolution, Å	18.9
Release Date	2019-12-04
Update Date	2024-03-27
Authors	Takizawa, Y., Ho, C.H., Tachiwana, H., Matsunami, H., Kobayashi, W., Suzuki, M., Arimura, Y., Hori, T., Fukagawa, T., Ohi, M.D., Wolf, M., Kurumizaka, H.
Publication	PMID: 31711756
doi	10.1016/j.str.2019.10.016
RCSB PDB	6L49
EMDB	EMD-0768
Q-score	0.071

Core histones in Nucleosome-like particles:

	Side	Chain	HistoneDB Variant	Taxa	UID
H3	Proximal	A	cenH3	Homo sapiens	P49450
H3	Distal	E	cenH3	Homo sapiens	P49450
H4	Proximal	B	canonical H4	Homo sapiens	P62805
H4	Distal	F	canonical H4	Homo sapiens	P62805
H2A	Proximal	C	canonical H2A	Homo sapiens	P04908
H2A	Distal	G	canonical H2A	Homo sapiens	P04908
H2B	Proximal	D	canonical H2B	Homo sapiens	P06899
H2B	Distal	H	canonical H2B	Homo sapiens	P06899

	Side	Chain	HistoneDB Variant	Taxa	UID
H3	Proximal	K	canonical H3	Homo sapiens	P68431
H3	Distal	O	canonical H3	Homo sapiens	P68431
H4	Proximal	L	canonical H4	Homo sapiens	P62805
H4	Distal	P	canonical H4	Homo sapiens	P62805
H2A	Proximal	M	canonical H2A	Homo sapiens	P04908
H2A	Distal	Q	canonical H2A	Homo sapiens	P04908
H2B	Proximal	N	canonical H2B	Homo sapiens	P06899
H2B	Distal	R	canonical H2B	Homo sapiens	P06899

	Side	Chain	HistoneDB Variant	Taxa	UID
H3	Proximal	S	canonical H3	Homo sapiens	P68431
H3	Distal	W	canonical H3	Homo sapiens	P68431
H4	Proximal	T	canonical H4	Homo sapiens	P62805
H4	Distal	X	canonical H4	Homo sapiens	P62805
H2A	Proximal	U	canonical H2A	Homo sapiens	P04908
H2A	Distal	Y	canonical H2A	Homo sapiens	P04908
H2B	Proximal	V	canonical H2B	Homo sapiens	P06899
H2B	Distal	Z	canonical H2B	Homo sapiens	P06899

DNA:

Chain	Variant	Length
I	601	485
J	601	485

H3

H4

H2A

H2B

DNA

Other

Orthographic Superimpose 1KX5 Show axes

Aligned nucleosome coordinates

X - Y

X - Z

Z - Y

Nucleosome reference frame definition

DNA relative twist and local base step parameters

3DNA

Relative Twist

Sequence on X-axis is numbered relative to the dyad base pair.

Atomic contacts between nucleosomal entities.

H3p chain A

H4p chain B

H2Ap chain C

H2Bp chain D

H3d chain E

H4d chain F

H2Ad chain G

H2Bd chain H

DNA top chain I, bot chain J

Hover the mouse cursor on the barplot to show contact information. Oncogenic mutations of non-histone proteins in contact are highlighted.